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For permits other than stormwater permits, the agencies issue effluent limitations for specific pollutants, pursuant to the Clean Water Act (CWA). The basis for these limitations depends on the type of discharging facility, the discharge characteristics and status of the specific surface water body receiving the discharge.

Some dischargers are subject to water quality-based effluent limitations, derived from water quality standards for the adjacent water body.

For pollutants not covered by the above circumstances, the agency may set technology-based limitations based on its "best professional judgment."[4]

Most NPDES permits require facilities to submit monthly DMRs, but some permits require seasonal or semi-annual reporting. Facilities may collect and analyze samples more frequently, e.g. weekly, and summarize the results for the prescribed reporting period. Permits typically require reporting of wastewater flow and the results of one or more chemical tests, such as pH, biochemical oxygen demand (BOD), total suspended solids (TSS), nutrients (nitrates and phosphorus), various toxic pollutants, temperature, etc. Some permits also require aquatic biomonitoring of the receiving waterbody.

The CWA defines DMR data as publicly available information (except for data that would reveal trade secrets).[5] EPA houses DMR data in two information systems, the Permit Compliance System (PCS) and the Integrated Compliance Information System (ICIS). These databases are available through EPA's "Envirofacts" website and Enforcement and Compliance History Online (ECHO).[6] EPA has also create the Discharge Monitoring Report (DMR) Pollutant Loading Tool to help users determine who is discharging, what pollutants they are discharging and how much, and where they are discharging. EPA also allows users to search on "who Facility-level data (which allows comparisons of a facility's air, water and solid waste compliance) are available through the agency’s Facility registry system.

^Note: Some permittees, notably stormwater dischargers such as construction site operators and municipal separate storm sewer systems, may not be required to file DMRs. These facilities prepare stormwater pollution prevention plans and may be required to submit other reports, which vary from state to state.